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Primary Tumor and Inter-Organ Augmentations for Supervised Lymph Node Colon Adenocarcinoma Metastasis Detection
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0003-0298-937X
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Sectra AB, Linkoping, Sweden.ORCID iD: 0000-0003-1066-3070
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).ORCID iD: 0000-0002-9217-9997
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).ORCID iD: 0000-0002-7765-1747
2021 (English)In: MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION - MICCAI 2021, PT V, SPRINGER INTERNATIONAL PUBLISHING AG , 2021, Vol. 12905, p. 624-633Conference paper, Published paper (Refereed)
Abstract [en]

The scarcity of labeled data is a major bottleneck for developing accurate and robust deep learning-based models for histopathology applications. The problem is notably prominent for the task of metastasis detection in lymph nodes, due to the tissues low tumor-to-non-tumor ratio, resulting in labor- and time-intensive annotation processes for the pathologists. This work explores alternatives on how to augment the training data for colon carcinoma metastasis detection when there is limited or no representation of the target domain. Through an exhaustive study of cross-validated experiments with limited training data availability, we evaluate both an inter-organ approach utilizing already available data for other tissues, and an intra-organ approach, utilizing the primary tumor. Both these approaches result in little to no extra annotation effort. Our results show that these data augmentation strategies can be an efficient way of increasing accuracy on metastasis detection, but fore-most increase robustness.

Place, publisher, year, edition, pages
SPRINGER INTERNATIONAL PUBLISHING AG , 2021. Vol. 12905, p. 624-633
Series
Lecture Notes in Computer Science, ISSN 0302-9743
Keywords [en]
Computer aided diagnosis; Computational pathology; Domain adaptation; Inter-organ; Colon cancer metastasis
National Category
Natural Language Processing
Identifiers
URN: urn:nbn:se:liu:diva-181214DOI: 10.1007/978-3-030-87240-3_60ISI: 000712025900060ISBN: 9783030872403 (print)ISBN: 9783030872397 (print)OAI: oai:DiVA.org:liu-181214DiVA, id: diva2:1613884
Conference
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), ELECTR NETWORK, sep 27-oct 01, 2021
Note

Funding Agencies|Wallenberg AI, Autonomous Systems and Software Program (WASP) - Knut and AliceWallenberg Foundation; strategic research environment ELLIIT; VINNOVAVinnova [2017-02447]

Available from: 2021-11-23 Created: 2021-11-23 Last updated: 2025-02-07
In thesis
1. Synthetic data for visual machine learning: A data-centric approach
Open this publication in new window or tab >>Synthetic data for visual machine learning: A data-centric approach
2022 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Deep learning allows computers to learn from observations, or else training data. Successful application development requires skills in neural network design, adequate computational resources, and a training data distribution that covers the application do-main. We are currently witnessing an artificial intelligence (AI) outbreak with enough computational power to train very deep networks and build models that achieve similar or better than human performance. The crucial factor for the algorithms to succeed has proven to be the training data fed to the learning process. Too little or low quality or out-of-the-target distribution data will lead to poorly performing models no matter the capacity and the data regularization methods.

This thesis is a data-centric approach to AI and presents a set of contributions related to synthesizing images for training supervised visual machine learning. It is motivated by the profound potential of synthetic data in cases of low availability of captured data, expensive acquisition and annotation, and privacy and ethical issues. The presented work aims to generate images similar to samples drawn from the target distribution and evaluate the generated data as the sole training data source and in conjunction with captured imagery. For this, two synthesis methods are explored: computer graphics and generative modeling. Computer graphics-based generation methods and synthetic datasets for computer vision tasks are thoroughly reviewed. In the same context, a system employing procedural modeling and physically-based rendering is introduced for data generation for urban scene understanding. The scheme is flexible, easily scalable, and produces complex and diverse images with pixel-perfect annotations at no cost. Generative Adversarial Networks (GANs) are also used to generate images for small data scenarios augmentation. The strategy advances the model’s performance and robustness. Finally, ensembles of independently trained GANs investigate ways to improve images’ diversity and create synthetic data to serve as the only training source.

The application areas of the presented contributions relate to two image modalities, natural and histopathology images, to cover different aspects in the generation methods and the tasks’ characteristics and requirements. There are showcased synthesized examples of natural images for automotive applications and weather classification, and histopathology images for breast cancer and colon adenocarcinoma metastasis detection. This thesis, as a whole, promotes data-centric supervised deep learning development by highlighting the potential of synthetic data as a training data resource. It emphasizes the control over the formation process, the ability of multi-modality formats, and the automatic generation of annotations.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2022. p. 115
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 2202
Keywords
Training data, Synthetic images, Computer graphics, Generative modeling, Natural images, Histopathology, Digital pathology, Machine learning, Deep learning
National Category
Medical Imaging
Identifiers
urn:nbn:se:liu:diva-182336 (URN)10.3384/9789179291754 (DOI)9789179291747 (ISBN)9789179291754 (ISBN)
Public defence
2022-02-14, Domteatern, Visualiseringscenter C, Kungsgatan 54, Norrköping, 09:15 (English)
Opponent
Supervisors
Note

ISBN for PDF has been added in the PDF-version.

Available from: 2022-01-17 Created: 2022-01-17 Last updated: 2025-02-09Bibliographically approved
2. Deep Learning for Digital Pathology in Limited Data Scenarios
Open this publication in new window or tab >>Deep Learning for Digital Pathology in Limited Data Scenarios
2022 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The impressive technical advances seen for machine learning algorithms in combination with the digitalization of medical images in the radiology and pathology departments show great promise in introducing powerful image analysis tools for image diagnostics. In particular, deep learning, a subfield within machine learning, has shown great success, advancing fields such as image classification and detection. However, these types of algorithms are only used to a very small extent in clinical practice. 

One reason is that the unique nature of radiology and pathology images and the clinical setting in which they are acquired poses challenges not seen in other image domains. Differences relate to capturing methods, as well as the image contents. In addition, these datasets are not only unique on a per-image basis but as a collective dataset. Characteristics such as size, class balance, and availability of annotated labels make creating robust and generalizable deep learning methods a challenge. 

This thesis investigates how deep learning models can be trained for applications in this domain, with particular focus on histopathology data. We investigate how domain shift between different scanners causes performance drop, and present ways of mitigating this. We also present a method to detect when domain shift occurs between different datasets. Another hurdle is the shortage of labeled data for medical applications, and this thesis looks at two different approaches to solving this problem. The first approach investigates how labeled data from one organ and cancer type can boost cancer classification in another organ where labeled data is scarce. The second approach looks at a specific type of unsupervised learning method, self-supervised learning, where the model is trained on unlabeled data. For both of these approaches, we present strategies to handle low-data regimes that may greatly increase the availability to build deep learning models for a wider range of applications. 

Furthermore, deep learning technology enables us to go beyond traditional medical domains, and combine the data from both radiology and pathology. This thesis presents a method for improved cancer characterization on contrast-enhanced CT by incorporating corresponding pathology data during training. The method shows the potential of im-proving future healthcare by intergraded diagnostics made possible by machine-learning technology. 

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2022. p. 60
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 2253
Keywords
Medical imaging, Digital pathology, Radiology, Machine learning, Deep learning.
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:liu:diva-189009 (URN)10.3384/9789179294748 (DOI)9789179294731 (ISBN)9789179294748 (ISBN)
Public defence
2022-11-14, Kåkenhus, K3, Campus Norrköping, Norrköping, 09:15 (English)
Opponent
Supervisors
Available from: 2022-10-07 Created: 2022-10-07 Last updated: 2023-04-03Bibliographically approved

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Tsirikoglou, ApostoliaStacke, KarinEilertsen, GabrielUnger, Jonas
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